Thanks for your posting on Q&A.
We could run the script to reindex the WSUS database. To do this, please follow the below steps:
First of all, we could open the SSMS as an administrator first. If there is no SSMS tool in your WSUS server, please follow this link and download one.
Then we could copy the reindex scripts in this link and run the scripts in the WSUS database - SUSDB.
Here is a reference picture for your reference:
Did your WSUS server integrated into the MECM? As far as I know, the script will be ran automatically when the SUP sync metadata from WSUS server next time.
Hope the above will be helpful.
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